{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:44:42Z","timestamp":1740185082048,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2016,12,16]],"date-time":"2016-12-16T00:00:00Z","timestamp":1481846400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["T32 HG002295\/HG\/NHGRI","U54CA143798","R01CA188228"],"award-info":[{"award-number":["T32 HG002295\/HG\/NHGRI","U54CA143798","R01CA188228"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"DFCI-Novartis Drug Discovery Program"},{"DOI":"10.13039\/100008221","name":"Cure Starts Now Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100008221","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>We present SeqLib, a C\u2009++\u2009API and command line tool that provides a rapid and user-friendly interface to BAM\/SAM\/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C\u2009++\u2009sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment.<\/jats:p>\n               <jats:p>Availability and Implementation: SeqLib is available on Linux and OSX for the C\u2009++98 standard and later at github.com\/walaj\/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw741","type":"journal-article","created":{"date-parts":[[2016,11,19]],"date-time":"2016-11-19T04:05:52Z","timestamp":1479528352000},"page":"751-753","source":"Crossref","is-referenced-by-count":13,"title":["SeqLib: a C\u2009++ API for rapid BAM manipulation, sequence alignment and sequence assembly"],"prefix":"10.1093","volume":"33","author":[{"given":"Jeremiah","family":"Wala","sequence":"first","affiliation":[{"name":"The Broad Institute of Harvard and MIT, Cambridge, MA, USA"},{"name":"Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA"},{"name":"Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA"}]},{"given":"Rameen","family":"Beroukhim","sequence":"additional","affiliation":[{"name":"The Broad Institute of Harvard and MIT, Cambridge, MA, USA"},{"name":"Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA, USA"},{"name":"Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,12,16]]},"reference":[{"key":"2023020204502013400_btw741-B1","doi-asserted-by":"crossref","first-page":"1691","DOI":"10.1093\/bioinformatics\/btr174","article-title":"BamTools: a C\u2009++ API and toolkit for analyzing and managing BAM files","volume":"27","author":"Barnett","year":"2011","journal-title":"Bioinformatics"},{"key":"2023020204502013400_btw741-B2","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1471-2105-9-11","article-title":"SeqAn An efficient, generic C\u2009++ library for sequence analysis","volume":"9","author":"D\u00f6ring","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023020204502013400_btw741-B3","article-title":"Haplotype-based variant detection from short-read sequencing","author":"Garrison","year":"2012","journal-title":"arXiv"},{"key":"2023020204502013400_btw741-B4","first-page":"656","article-title":"BLAT\u2013the BLAST-like alignment tool","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res"},{"key":"2023020204502013400_btw741-B5","first-page":"1","article-title":"Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM","author":"Li","year":"2015","journal-title":"arXiv"},{"key":"2023020204502013400_btw741-B6","doi-asserted-by":"crossref","first-page":"2885","DOI":"10.1093\/bioinformatics\/btv290","article-title":"BFC: correcting Illumina sequencing errors","volume":"31","author":"Li","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020204502013400_btw741-B7","doi-asserted-by":"crossref","first-page":"1838","DOI":"10.1093\/bioinformatics\/bts280","article-title":"Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly","volume":"28","author":"Li","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020204502013400_btw741-B8","doi-asserted-by":"crossref","first-page":"2029","DOI":"10.1093\/bioinformatics\/btw111","article-title":"VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules","volume":"32","author":"Wala","year":"2016","journal-title":"Bioinformatics"},{"year":"2016","author":"Morgan","key":"2023020204502013400_btw741-B9"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/5\/751\/49037525\/bioinformatics_33_5_751.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/5\/751\/49037525\/bioinformatics_33_5_751.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T04:51:18Z","timestamp":1675313478000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/5\/751\/2571356"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2016,12,16]]},"references-count":9,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2017,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btw741","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2017,3,1]]},"published":{"date-parts":[[2016,12,16]]}}}